pyvlasiator 0.1.3__tar.gz → 0.1.5__tar.gz

{pyvlasiator-0.1.3 → pyvlasiator-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: pyvlasiator
-Version: 0.1.3
+Version: 0.1.5
 Summary: Python utilities for processing Vlasiator data
 Author: Hongyang Zhou
 Author-email: hyzhou@umich.edu
@@ -17,6 +17,9 @@ Description-Content-Type: text/markdown
 # pyvlasiator
 
 <p align="center">
+  <a href="https://badge.fury.io/py/pyvlasiator">
+    <img src="https://badge.fury.io/py/pyvlasiator.svg" alt="PyPI version" height="18">
+  </a>
   <a href="https://github.com/henry2004y/pyvlasiator/actions">
     <img src="https://github.com/henry2004y/pyvlasiator/actions/workflows/CI.yml/badge.svg">
   </a>
@@ -31,7 +34,7 @@ Description-Content-Type: text/markdown
   </a>
 </p>
 
-Lightweight Python package for processing Vlasiator data.
+Lightweight Python package for processing [Vlasiator](https://github.com/fmihpc/vlasiator) data, alternative to [Analysator](https://github.com/fmihpc/analysator).
 
 ## Installation
 

{pyvlasiator-0.1.3 → pyvlasiator-0.1.5}/README.md

@@ -1,6 +1,9 @@
 # pyvlasiator
 
 <p align="center">
+  <a href="https://badge.fury.io/py/pyvlasiator">
+    <img src="https://badge.fury.io/py/pyvlasiator.svg" alt="PyPI version" height="18">
+  </a>
   <a href="https://github.com/henry2004y/pyvlasiator/actions">
     <img src="https://github.com/henry2004y/pyvlasiator/actions/workflows/CI.yml/badge.svg">
   </a>
@@ -15,7 +18,7 @@
   </a>
 </p>
 
-Lightweight Python package for processing Vlasiator data.
+Lightweight Python package for processing [Vlasiator](https://github.com/fmihpc/vlasiator) data, alternative to [Analysator](https://github.com/fmihpc/analysator).
 
 ## Installation
 

{pyvlasiator-0.1.3 → pyvlasiator-0.1.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyvlasiator"
-version = "0.1.3"
+version = "0.1.5"
 description = "Python utilities for processing Vlasiator data"
 authors = ["Hongyang Zhou <hyzhou@umich.edu>"]
 readme = "README.md"

{pyvlasiator-0.1.3 → pyvlasiator-0.1.5}/src/pyvlasiator/plot/__init__.py

@@ -12,4 +12,6 @@ from pyvlasiator.plot.plot import (
     contourf,
     streamplot,
     vdfslice,
+    AxisUnit,
+    ColorScale,
 )

{pyvlasiator-0.1.3 → pyvlasiator-0.1.5}/src/pyvlasiator/plot/plot.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import numpy as np
+from numpy.typing import ArrayLike
 import math
 import warnings
 from typing import Callable
@@ -8,7 +9,7 @@ from collections import namedtuple
 from enum import Enum
 from pyvlasiator.vlsv import Vlsv
 from pyvlasiator.vlsv.reader import _getdim2d
-from pyvlasiator.vlsv.variables import RE
+from pyvlasiator.vlsv.variables import RE, RMERCURY
 
 
 class ColorScale(Enum):
@@ -35,8 +36,10 @@ class AxisUnit(Enum):
         - SI (2): Units from the International System of Units (SI), such as meters, seconds, kilograms, etc.
     """
 
-    EARTH = 1
-    SI = 2
+    SI = 1
+    KSI = 2
+    EARTH = 3
+    MERCURY = 4
 
 
 # Plotting arguments
@@ -182,6 +185,7 @@ def _plot1d(
 
     return c
 
+
 def pcolormesh(
     self: Vlsv,
     var: str = "",
@@ -609,8 +613,12 @@ def set_args(
 
     if axisunit == AxisUnit.EARTH:
         unitstr = r"$R_E$"
-    else:
-        unitstr = r"$m$"
+    elif axisunit == AxisUnit.SI:
+        unitstr = "m"
+    elif axisunit == AxisUnit.MERCURY:
+        unitstr = r"$R_M$"
+    elif axisunit == AxisUnit.KSI:
+        unitstr = "km"
     strx = axislabels[0] + " [" + unitstr + "]"
     stry = axislabels[1] + " [" + unitstr + "]"
 
@@ -771,7 +779,15 @@ def get_axis(axisunit: AxisUnit, plotrange: tuple, sizes: tuple) -> tuple:
         A tuple containing the x and y axis coordinates.
     """
 
-    scale_factor = 1.0 / RE if axisunit == AxisUnit.EARTH else 1.0
+    if axisunit == AxisUnit.EARTH:
+        scale_factor = 1.0 / RE
+    elif axisunit == AxisUnit.MERCURY:
+        scale_factor = 1.0 / RMERCURY
+    elif axisunit == AxisUnit.KSI:
+        scale_factor = 1.0 / 1e3
+    else:  # SI
+        scale_factor = 1.0
+
     start = tuple(s * scale_factor for s in plotrange[:2])
     stop = tuple(s * scale_factor for s in plotrange[2:])
 
@@ -794,7 +810,6 @@ def set_colorbar(
     v2: float = np.nan,
     data: np.ndarray = np.array([1.0]),
     linthresh: float = 1.0,
-    logstep: float = 1.0,
     linscale: float = 0.03,
 ):
     """
@@ -816,8 +831,6 @@ def set_colorbar(
         not provided. Defaults to np.array([1.0]).
     linthresh: float, optional
         The threshold value for symmetric log color scales. Defaults to 1.0.
-    logstep: float, optional
-        The step size for tick values in log color scales. Defaults to 1.0.
     linscale: float, optional
         A scaling factor for linear regions in symmetric log color scales.
         Defaults to 0.03.
@@ -833,10 +846,6 @@ def set_colorbar(
     ------
     ValueError
         If an invalid colorscale type is provided.
-
-    Notes
-    -----
-    - The 'SymLog' colorscale is currently not fully implemented.
     """
     import matplotlib
 
@@ -849,13 +858,10 @@ def set_colorbar(
         norm = matplotlib.colors.LogNorm(vmin, vmax)
         ticks = matplotlib.ticker.LogLocator(base=10, subs=range(0, 9))
     else:  # symmetric log
-        logthresh = int(math.floor(math.log10(linthresh)))
-        minlog = int(math.ceil(math.log10(-vmin)))
-        maxlog = int(math.ceil(math.log10(vmax)))
-        # TODO: fix this!
-        # norm = matplotlib.colors.SymLogNorm(linthresh, linscale, vmin, vmax, base=10)
-        # ticks = [ [-(10.0**x) for x in minlog:-logstep:logthresh]..., 0.0,
-        #   [10.0**x for x in logthresh:logstep:maxlog]..., ]
+        norm = matplotlib.colors.SymLogNorm(
+            linthresh=linthresh, linscale=linscale, vmin=vmin, vmax=vmax, base=10
+        )
+        ticks = matplotlib.ticker.SymmetricalLogLocator(linthresh=linthresh, base=10)
 
     return norm, ticks
 
@@ -922,7 +928,6 @@ def vdfslice(
     meta: Vlsv,
     location: tuple | list,
     ax=None,
-    limits: tuple = (float("-inf"), float("inf"), float("-inf"), float("inf")),
     verbose: bool = False,
     species: str = "proton",
     unit: AxisUnit = AxisUnit.SI,
@@ -967,7 +972,15 @@ def vdfslice(
 
     norm = matplotlib.colors.LogNorm(vmin, vmax)
 
-    h = ax.hist2d(v1, v2, bins=(r1, r2), weights=weights, norm=norm, shading="flat")
+    h = ax.hist2d(
+        v1,
+        v2,
+        bins=(r1, r2),
+        weights=weights,
+        norm=norm,
+        shading="flat",
+        **kwargs,
+    )
 
     ax.set_title(str_title, fontweight="bold")
     ax.set_xlabel(strx)
@@ -1012,6 +1025,10 @@ def prep_vdf(
 
     if unit == AxisUnit.EARTH:
         location = [loc * RE for loc in location]
+    elif unit == AxisUnit.MERCURY:
+        location = [loc * RMERCURY for loc in location]
+    elif unit == AxisUnit.KSI:
+        location = [loc * 1e3 for loc in location]
 
     # Set unit conversion factor
     unitvfactor = 1e3 if unitv == "km/s" else 1.0

{pyvlasiator-0.1.3 → pyvlasiator-0.1.5}/src/pyvlasiator/vlsv/reader.py

@@ -375,16 +375,17 @@ class Vlsv:
         """
         Read variables as numpy arrays from the open vlsv file.
 
-        Parameters
-        ----------
-        cellids : int or list[int] or np.ndarray
-            If -1 then all data is read. If nonzero then only the vector for the specified
-            cell id or cellids is read.
-        sorted : bool
-            If the returned array is sorted by cell IDs. Only applied for full arrays.
-        Returns
-        -------
-        numpy.ndarray
+        Args:
+            name (str): The name of the variable to read.
+            cellids (int, list[int], np.ndarray, optional):
+                Specifies which cell IDs to read data for. Defaults to -1, which reads data for all cells.
+            - If an integer (except -1), only the data for that specific cell ID is read.
+            - If a list or NumPy array of integers, only the data for the specified cell IDs are read.
+            - Specifying cell IDs is not supported for "FSgrid" or "ionosphere" variables.
+            sorted (bool, optional): If True, the returned array is sorted by cell IDs (only applicable when reading all cells, cellids=-1). Defaults to True.
+
+        Returns:
+            numpy.ndarray
         """
 
         if self.has_variable(name) and name.startswith("fg_"):

{pyvlasiator-0.1.3 → pyvlasiator-0.1.5}/src/pyvlasiator/vlsv/variables.py

@@ -11,6 +11,7 @@ MU0 = 4 * pi * 1e-7  # Vacuum permeability, [H/m]
 EPSILON0 = 1 / (C**2 * MU0)  # Vacuum permittivity, [F/m]
 KB = 1.38064852e-23  # Boltzmann constant, [m²kg/(s²K)]
 RE = 6.371e6  # Earth radius, [m]
+RMERCURY = 4.8794e6 # Mercury radius, [m]
 
 speciesdict = {
     "avgs": "p",